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- PDB-5qc8: Crystal structure of human Cathepsin-S with bound ligand -

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Basic information

Entry
Database: PDB / ID: 5qc8
TitleCrystal structure of human Cathepsin-S with bound ligand
ComponentsCathepsin S
KeywordsHYDROLASE / D3R / Cathepsin S / Ligand Docking
Function / homology
Function and homology information


cathepsin S / basement membrane disassembly / positive regulation of cation channel activity / antigen processing and presentation of peptide antigen / endolysosome lumen / response to acidic pH / cellular response to thyroid hormone stimulus / Trafficking and processing of endosomal TLR / proteoglycan binding / Assembly of collagen fibrils and other multimeric structures ...cathepsin S / basement membrane disassembly / positive regulation of cation channel activity / antigen processing and presentation of peptide antigen / endolysosome lumen / response to acidic pH / cellular response to thyroid hormone stimulus / Trafficking and processing of endosomal TLR / proteoglycan binding / Assembly of collagen fibrils and other multimeric structures / toll-like receptor signaling pathway / cysteine-type endopeptidase activator activity involved in apoptotic process / antigen processing and presentation / fibronectin binding / collagen catabolic process / extracellular matrix disassembly / phagocytic vesicle / laminin binding / collagen binding / MHC class II antigen presentation / Degradation of the extracellular matrix / lysosomal lumen / proteolysis involved in protein catabolic process / Endosomal/Vacuolar pathway / positive regulation of apoptotic signaling pathway / protein processing / antigen processing and presentation of exogenous peptide antigen via MHC class II / late endosome / tertiary granule lumen / collagen-containing extracellular matrix / ficolin-1-rich granule lumen / adaptive immune response / lysosome / immune response / cysteine-type endopeptidase activity / intracellular membrane-bounded organelle / serine-type endopeptidase activity / Neutrophil degranulation / proteolysis / extracellular space / extracellular region
Similarity search - Function
Cathepsin propeptide inhibitor domain (I29) / Cathepsin propeptide inhibitor domain (I29) / Cathepsin propeptide inhibitor domain (I29) / Papain-like cysteine endopeptidase / Cysteine peptidase, asparagine active site / Eukaryotic thiol (cysteine) proteases asparagine active site. / Cysteine peptidase, histidine active site / Eukaryotic thiol (cysteine) proteases histidine active site. / : / Peptidase C1A, papain C-terminal ...Cathepsin propeptide inhibitor domain (I29) / Cathepsin propeptide inhibitor domain (I29) / Cathepsin propeptide inhibitor domain (I29) / Papain-like cysteine endopeptidase / Cysteine peptidase, asparagine active site / Eukaryotic thiol (cysteine) proteases asparagine active site. / Cysteine peptidase, histidine active site / Eukaryotic thiol (cysteine) proteases histidine active site. / : / Peptidase C1A, papain C-terminal / Papain family cysteine protease / Papain family cysteine protease / Cysteine proteinases / Cysteine peptidase, cysteine active site / Eukaryotic thiol (cysteine) proteases cysteine active site. / Cathepsin B; Chain A / Papain-like cysteine peptidase superfamily / Alpha-Beta Complex / Alpha Beta
Similarity search - Domain/homology
Chem-BFV / Cathepsin S
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.74 Å
Model detailsStructures re-refined for D3R docking challenge
AuthorsBembenek, S.D. / Ameriks, M.K. / Mirzadegan, T. / Yang, H. / Shao, C. / Burley, S.K.
CitationJournal: To be published
Title: Crystal structure of human Cathepsin-S with bound ligand
Authors: Bembenek, S.D. / Ameriks, M.K. / Mirzadegan, T. / Yang, H. / Shao, C. / Burley, S.K.
History
DepositionAug 4, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 20, 2017Provider: repository / Type: Initial release
Revision 1.1Feb 21, 2018Group: Structure summary / Category: pdbx_deposit_group / Item: _pdbx_deposit_group.group_type
Revision 2.0Jun 6, 2018Group: Atomic model / Data collection ...Atomic model / Data collection / Derived calculations / Other / Refinement description / Structure summary
Category: atom_site / atom_sites ...atom_site / atom_sites / pdbx_nonpoly_scheme / pdbx_poly_seq_scheme / refine / refine_hist / refine_ls_shell / reflns / struct_site / struct_site_gen
Item: _atom_site.occupancy / _atom_sites.fract_transf_matrix[2][1] ..._atom_site.occupancy / _atom_sites.fract_transf_matrix[2][1] / _atom_sites.fract_transf_matrix[3][2] / _pdbx_nonpoly_scheme.auth_mon_id / _pdbx_nonpoly_scheme.auth_seq_num / _pdbx_poly_seq_scheme.auth_mon_id / _refine.B_iso_mean / _refine.aniso_B[1][2] / _refine.aniso_B[2][3] / _refine.details / _refine.ls_R_factor_R_free / _refine.ls_R_factor_R_work / _refine.ls_R_factor_obs / _refine.ls_percent_reflns_obs / _refine_hist.cycle_id / _refine_ls_shell.d_res_high / _refine_ls_shell.d_res_low / _reflns.percent_possible_obs / _struct_site.pdbx_num_residues
Revision 2.1Feb 10, 2021Group: Database references / Structure summary / Category: audit_author / citation_author
Item: _audit_author.identifier_ORCID / _citation_author.identifier_ORCID
Revision 2.2Nov 17, 2021Group: Advisory / Database references / Structure summary
Category: database_2 / pdbx_deposit_group / pdbx_unobs_or_zero_occ_atoms
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_deposit_group.group_description
Revision 2.3Oct 23, 2024Group: Data collection / Refinement description / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_entry_details / pdbx_modification_feature / struct_ncs_dom_lim
Item: _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id ..._struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Cathepsin S
B: Cathepsin S
hetero molecules


Theoretical massNumber of molelcules
Total (without water)50,3494
Polymers49,0332
Non-polymers1,3172
Water9,962553
1
A: Cathepsin S
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,1752
Polymers24,5161
Non-polymers6581
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Cathepsin S
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,1752
Polymers24,5161
Non-polymers6581
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)91.062, 37.153, 127.677
Angle α, β, γ (deg.)90.00, 93.14, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-1186-

HOH

21B-1224-

HOH

Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B

NCS domain segments:

Component-ID: _ / Ens-ID: 1 / Beg auth comp-ID: ILE / Beg label comp-ID: ILE / End auth comp-ID: GLY / End label comp-ID: GLY / Refine code: _ / Auth seq-ID: 0 - 220 / Label seq-ID: 1 - 221

Dom-IDAuth asym-IDLabel asym-ID
1AA
2BB

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Components

#1: Protein Cathepsin S


Mass: 24516.471 Da / Num. of mol.: 2 / Mutation: C139S
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CTSS / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: P25774, cathepsin S
#2: Chemical ChemComp-BFV / N-benzyl-1-{3-[(2-chloro-5-{5-(methylsulfonyl)-1-[3-(morpholin-4-yl)propyl]-4,5,6,7-tetrahydro-1H-pyrazolo[4,3-c]pyridin-3-yl}phenyl)ethynyl]phenyl}methanamine


Mass: 658.252 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C36H40ClN5O3S
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 553 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.21 Å3/Da / Density % sol: 44.42 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 4.5
Details: 100MM SODIUM ACETATE PH 4.5, 200MM AMMONIUM ACETATE, 25% PEG 8000. PROTEIN CONCENTRATION 7 MG/ML, VAPOR DIFFUSION, SITTING DROP, TEMPERATURE 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.54178
DetectorType: RIGAKU SATURN 944 / Detector: CCD / Date: May 10, 2006
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54178 Å / Relative weight: 1
ReflectionResolution: 1.74→45.46 Å / Num. obs: 38560 / % possible obs: 91.8 %

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
REFMAC5.8.0158refinement
PDB_EXTRACT3.23data extraction
MOSFLMdata reduction
SCALAdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.74→45.46 Å / Cor.coef. Fo:Fc: 0.956 / Cor.coef. Fo:Fc free: 0.935 / SU B: 2.425 / SU ML: 0.078 / Cross valid method: THROUGHOUT / ESU R: 0.129 / ESU R Free: 0.117 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.198 2039 5 %RANDOM
Rwork0.167 ---
obs0.169 38560 91.8 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 13.79 Å2
Baniso -1Baniso -2Baniso -3
1-0.25 Å20 Å20.09 Å2
2---0.09 Å20 Å2
3----0.17 Å2
Refinement stepCycle: LAST / Resolution: 1.74→45.46 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3395 0 92 553 4040
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0193585
X-RAY DIFFRACTIONr_bond_other_d0.0020.023119
X-RAY DIFFRACTIONr_angle_refined_deg1.4071.9234860
X-RAY DIFFRACTIONr_angle_other_deg0.9352.9887259
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.6525440
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.67624.472161
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.77615547
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.0211514
X-RAY DIFFRACTIONr_chiral_restr0.0860.2484
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.024052
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02760
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.8781.1551766
X-RAY DIFFRACTIONr_mcbond_other0.8751.1541765
X-RAY DIFFRACTIONr_mcangle_it1.3781.7272204
X-RAY DIFFRACTIONr_mcangle_other1.3781.7272205
X-RAY DIFFRACTIONr_scbond_it1.6331.4091819
X-RAY DIFFRACTIONr_scbond_other1.6331.4081820
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other2.6112.0272657
X-RAY DIFFRACTIONr_long_range_B_refined4.88315.3364334
X-RAY DIFFRACTIONr_long_range_B_other4.43214.2574153
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Ens-ID: 1 / Number: 14498 / Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Rms dev position: 0.07 Å / Weight position: 0.05

Dom-IDAuth asym-ID
1A
2B
LS refinement shellResolution: 1.74→1.79 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.258 112 -
Rwork0.237 2288 -
obs--73.94 %

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